public class RefSeqParser extends Object implements TranscriptParser
Constructor and Description |
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RefSeqParser(ReferenceDictionary refDict,
String basePath,
org.ini4j.Profile.Section iniSection) |
Modifier and Type | Method and Description |
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com.google.common.collect.ImmutableList<TranscriptModel> |
run() |
public RefSeqParser(ReferenceDictionary refDict, String basePath, org.ini4j.Profile.Section iniSection)
refDict
- path to ReferenceDictionary
to use for name/id and id/length mapping.basePath
- path to where the to-be-parsed files liveiniSection
- Profile.Section
with configuration from INI filepublic com.google.common.collect.ImmutableList<TranscriptModel> run() throws TranscriptParseException
run
in interface TranscriptParser
TranscriptModel
objects as parsed from the input.TranscriptParseException
- on problems with parsing the transcript filesCopyright © 2016. All rights reserved.